def get_intersection_of_3_set(): from biana.biana_commands import administration, available_sessions, create_new_session from biana.BianaObjects import BianaSessionManager import biana.utilities.identifier_utilities as id_utils create_new_session(sessionID="biana_session",dbname=DB_NAME, dbhost=DB_HOST, dbuser=DB_USER, dbpassword=DB_PASS, unification_protocol=UNIFICATION_PROTOCOL) objSession = available_sessions["biana_session"] objSession.create_new_user_entity_set( identifier_description_list = id_utils.read_identifier_list_from_file(BONE_FILE, id_type="uniprotaccession"), external_entity_attribute_restriction_list=[("taxid","9606")], id_type="embedded",new_user_entity_set_id="bone") objSession.create_new_user_entity_set( identifier_description_list = id_utils.read_identifier_list_from_file(LIVER_FILE, id_type="uniprotaccession"), external_entity_attribute_restriction_list=[("taxid","9606")], id_type="embedded",new_user_entity_set_id="liver") objSession.create_new_user_entity_set( identifier_description_list = id_utils.read_identifier_list_from_file(LUNG_FILE, id_type="uniprotaccession"), external_entity_attribute_restriction_list=[("taxid","9606")], id_type="embedded",new_user_entity_set_id="lung") print "Bone - Liver - Lung User Entity Sets are created..", objSession objSession.create_network( user_entity_set_id = "bone" , level = 1 , relation_type_list=["complex","interaction","pathway","reaction"] , include_relations_last_level = True , use_self_relations = False) objSession.create_network( user_entity_set_id = "liver" , level = 1 , relation_type_list=["complex","interaction","pathway","reaction"] , include_relations_last_level = True , use_self_relations = False) objSession.create_network( user_entity_set_id = "lung" , level = 1 , relation_type_list=["complex","interaction","pathway","reaction"] , include_relations_last_level = True , use_self_relations = False) print "Bone - Liver - Lung Networks are created..", objSession objSession.get_intersection_of_user_entity_set_list([objSession.get_user_entity_set("bone"), objSession.get_user_entity_set("liver"), objSession.get_user_entity_set("lung")], include_relations=True, new_user_entity_set_id="intersection") objSession.get_intersection_of_user_entity_set_list([objSession.get_user_entity_set("bone"), objSession.get_user_entity_set("liver")], include_relations=True, new_user_entity_set_id="bone_liver") objSession.get_intersection_of_user_entity_set_list([objSession.get_user_entity_set("bone"), objSession.get_user_entity_set("lung")], include_relations=True, new_user_entity_set_id="bone_lung") objSession.get_intersection_of_user_entity_set_list([objSession.get_user_entity_set("liver"), objSession.get_user_entity_set("lung")], include_relations=True, new_user_entity_set_id="liver_lung") print "Intersections are created..", objSession return
def get_seed_connected_nodes(): from biana.biana_commands import administration, available_sessions, create_new_session from biana.BianaObjects import BianaSessionManager import sets import biana.utilities.identifier_utilities as id_utils t_init = time.clock() relation_type_list = ["interaction"] # ["reaction","complex","pathway","interaction"] # Create a new BIANA session create_new_session(sessionID="biana_session",dbname=DB_NAME, dbhost=DB_HOST, dbuser=DB_USER, dbpassword=DB_PASS, unification_protocol=UNIFICATION_PROTOCOL) objSession = available_sessions["biana_session"] #identifier_description_list = id_utils.read_identifier_list_from_file("/home/emre/arastirma/colloboration/seeds_intracranial_and_aneurysm_and_mesh_genetics.txt", "genesymbol") identifier_description_list = id_utils.read_identifier_list_from_file("/home/emre/arastirma/colloboration/subarachnoid_and_hemorrhage_or_haemorrhage_and_mesh_genetics.seeds", "genesymbol") # Create a new User Entity Set (group of biomolecules) in this session uESet1 = objSession.create_new_user_entity_set( identifier_description_list = identifier_description_list, external_entity_attribute_restriction_list=[("taxid","9606")], id_type="embedded", new_user_entity_set_id="User_Entity_Set_1") t_1 = time.clock() # Get relations of biomolecules in this set objSession.create_network( user_entity_set_id = "User_Entity_Set_1" , level = 1, relation_type_list= relation_type_list, include_relations_last_level = False, use_self_relations = False) t_2 = time.clock() print "t_network:", t_2-t_1 # Select seeds and nodes connected by seeds in the network of this User Entity Set user_entities_to_print = sets.Set(uESet1.get_user_entity_ids(level=0))|uESet1.get_user_entity_ids_by_linker_degree_cutoff(2) objSession.select_user_entities_from_user_entity_set("User_Entity_Set_1", user_entities_to_print, clear_previous_selection=True) objSession.tag_selected_user_entities(user_entity_set_id="User_Entity_Set_1", tag="seed+connected") t_3 = time.clock() print "t_connected:", t_3-t_2 # Output set details - only selected nodes #objSession.output_user_entity_set_details(user_entity_set_id = "User_Entity_Set_1", out_method = open("nodes_selected.out", "w").write, attributes=["genesymbol", "uniprotaccession", "hgnc"], include_level_info=True, include_degree_info=True, level=None, only_selected=True, output_format="tabulated", include_tags_info = True, include_tags_linkage_degree_info=[], substitute_node_attribute_if_not_exists=True, output_1_value_per_attribute=False, include_command_in_rows=False) # Output set details - all nodes objSession.output_user_entity_set_details(user_entity_set_id = "User_Entity_Set_1", out_method = open("nodes.out", "w").write, attributes=["genesymbol", "uniprotaccession", "hgnc"], include_level_info=True, include_degree_info=True, level=None, only_selected=False, output_format="tabulated", include_tags_info = True, include_tags_linkage_degree_info=[], substitute_node_attribute_if_not_exists=True, output_1_value_per_attribute=False, include_command_in_rows=False) t_4 = time.clock() print "t_nodes:", t_4-t_3 # Output network details objSession.output_user_entity_set_network(user_entity_set_id = "User_Entity_Set_1", out_method=open("network.out", "w").write, node_attributes = [], participant_attributes = [], relation_attributes=["Method_id"], allowed_relation_types="all", include_relation_ids=False, include_participant_ids=True, include_relation_type=True, include_relation_sources=True, output_1_value_per_attribute=False, output_format="tabulated", only_selected=False, substitute_node_attribute_if_not_exists=True, include_participant_tags=False, include_relation_tags = False, include_unconnected_nodes=False) t_5 = time.clock() print "t_network:", t_5-t_4
def get_intersection_of_3_set(): from biana.biana_commands import administration, available_sessions, create_new_session from biana.BianaObjects import BianaSessionManager import biana.utilities.identifier_utilities as id_utils create_new_session(sessionID="biana_session", dbname=DB_NAME, dbhost=DB_HOST, dbuser=DB_USER, dbpassword=DB_PASS, unification_protocol=UNIFICATION_PROTOCOL) objSession = available_sessions["biana_session"] objSession.create_new_user_entity_set( identifier_description_list=id_utils.read_identifier_list_from_file( BONE_FILE, id_type="uniprotaccession"), external_entity_attribute_restriction_list=[("taxid", "9606")], id_type="embedded", new_user_entity_set_id="bone") objSession.create_new_user_entity_set( identifier_description_list=id_utils.read_identifier_list_from_file( LIVER_FILE, id_type="uniprotaccession"), external_entity_attribute_restriction_list=[("taxid", "9606")], id_type="embedded", new_user_entity_set_id="liver") objSession.create_new_user_entity_set( identifier_description_list=id_utils.read_identifier_list_from_file( LUNG_FILE, id_type="uniprotaccession"), external_entity_attribute_restriction_list=[("taxid", "9606")], id_type="embedded", new_user_entity_set_id="lung") print "Bone - Liver - Lung User Entity Sets are created..", objSession objSession.create_network( user_entity_set_id="bone", level=1, relation_type_list=["complex", "interaction", "pathway", "reaction"], include_relations_last_level=True, use_self_relations=False) objSession.create_network( user_entity_set_id="liver", level=1, relation_type_list=["complex", "interaction", "pathway", "reaction"], include_relations_last_level=True, use_self_relations=False) objSession.create_network( user_entity_set_id="lung", level=1, relation_type_list=["complex", "interaction", "pathway", "reaction"], include_relations_last_level=True, use_self_relations=False) print "Bone - Liver - Lung Networks are created..", objSession objSession.get_intersection_of_user_entity_set_list( [ objSession.get_user_entity_set("bone"), objSession.get_user_entity_set("liver"), objSession.get_user_entity_set("lung") ], include_relations=True, new_user_entity_set_id="intersection") objSession.get_intersection_of_user_entity_set_list( [ objSession.get_user_entity_set("bone"), objSession.get_user_entity_set("liver") ], include_relations=True, new_user_entity_set_id="bone_liver") objSession.get_intersection_of_user_entity_set_list( [ objSession.get_user_entity_set("bone"), objSession.get_user_entity_set("lung") ], include_relations=True, new_user_entity_set_id="bone_lung") objSession.get_intersection_of_user_entity_set_list( [ objSession.get_user_entity_set("liver"), objSession.get_user_entity_set("lung") ], include_relations=True, new_user_entity_set_id="liver_lung") print "Intersections are created..", objSession return
def get_seed_connected_nodes(): from biana.biana_commands import administration, available_sessions, create_new_session from biana.BianaObjects import BianaSessionManager import sets import biana.utilities.identifier_utilities as id_utils t_init = time.clock() relation_type_list = ["interaction" ] # ["reaction","complex","pathway","interaction"] # Create a new BIANA session create_new_session(sessionID="biana_session", dbname=DB_NAME, dbhost=DB_HOST, dbuser=DB_USER, dbpassword=DB_PASS, unification_protocol=UNIFICATION_PROTOCOL) objSession = available_sessions["biana_session"] #identifier_description_list = id_utils.read_identifier_list_from_file("/home/emre/arastirma/colloboration/seeds_intracranial_and_aneurysm_and_mesh_genetics.txt", "genesymbol") identifier_description_list = id_utils.read_identifier_list_from_file( "/home/emre/arastirma/colloboration/subarachnoid_and_hemorrhage_or_haemorrhage_and_mesh_genetics.seeds", "genesymbol") # Create a new User Entity Set (group of biomolecules) in this session uESet1 = objSession.create_new_user_entity_set( identifier_description_list=identifier_description_list, external_entity_attribute_restriction_list=[("taxid", "9606")], id_type="embedded", new_user_entity_set_id="User_Entity_Set_1") t_1 = time.clock() # Get relations of biomolecules in this set objSession.create_network(user_entity_set_id="User_Entity_Set_1", level=1, relation_type_list=relation_type_list, include_relations_last_level=False, use_self_relations=False) t_2 = time.clock() print "t_network:", t_2 - t_1 # Select seeds and nodes connected by seeds in the network of this User Entity Set user_entities_to_print = sets.Set(uESet1.get_user_entity_ids( level=0)) | uESet1.get_user_entity_ids_by_linker_degree_cutoff(2) objSession.select_user_entities_from_user_entity_set( "User_Entity_Set_1", user_entities_to_print, clear_previous_selection=True) objSession.tag_selected_user_entities( user_entity_set_id="User_Entity_Set_1", tag="seed+connected") t_3 = time.clock() print "t_connected:", t_3 - t_2 # Output set details - only selected nodes #objSession.output_user_entity_set_details(user_entity_set_id = "User_Entity_Set_1", out_method = open("nodes_selected.out", "w").write, attributes=["genesymbol", "uniprotaccession", "hgnc"], include_level_info=True, include_degree_info=True, level=None, only_selected=True, output_format="tabulated", include_tags_info = True, include_tags_linkage_degree_info=[], substitute_node_attribute_if_not_exists=True, output_1_value_per_attribute=False, include_command_in_rows=False) # Output set details - all nodes objSession.output_user_entity_set_details( user_entity_set_id="User_Entity_Set_1", out_method=open("nodes.out", "w").write, attributes=["genesymbol", "uniprotaccession", "hgnc"], include_level_info=True, include_degree_info=True, level=None, only_selected=False, output_format="tabulated", include_tags_info=True, include_tags_linkage_degree_info=[], substitute_node_attribute_if_not_exists=True, output_1_value_per_attribute=False, include_command_in_rows=False) t_4 = time.clock() print "t_nodes:", t_4 - t_3 # Output network details objSession.output_user_entity_set_network( user_entity_set_id="User_Entity_Set_1", out_method=open("network.out", "w").write, node_attributes=[], participant_attributes=[], relation_attributes=["Method_id"], allowed_relation_types="all", include_relation_ids=False, include_participant_ids=True, include_relation_type=True, include_relation_sources=True, output_1_value_per_attribute=False, output_format="tabulated", only_selected=False, substitute_node_attribute_if_not_exists=True, include_participant_tags=False, include_relation_tags=False, include_unconnected_nodes=False) t_5 = time.clock() print "t_network:", t_5 - t_4